Problems of taxonomy and phylogeny

Dormidont, no need to hide behind the mask of an amateur. You're a professional biologist.

I do have a biological education, but I haven't been involved in this field of human activity for several years . My study of insects is rather amateur in nature, since I do not belong to either scientific or educational institutions . I'm a retired biologist, if you like .

I feel sorry for my time spent philosophizing or discussing commonplaces about how bedbugs see the world or how perfect amoebas are.

It is from philosophy that science was born, and I think the denial of philosophical categories, the inability to look at biological science "from above", is a big minus of modern scientists. In my opinion, a scientist should accept any proven probability.

Dogmatism? An interesting accusation. Recently, I heard a man passionately accused of dogmatism who denied telekinesis and some other devilry, in a word, that the world works differently from what is taught at Moscow State University or St. Petersburg State University

I'll give you another example: in the 90s, a dolphin's body was found on Karadag with bite marks from a very large animal. And this is a fact, even an act was drawn up and sketched about it. We invited specialists to take a look. And they were accused in absentia of anti-scientific activities, without even coming to look at a really established fact! Isn't that dogmatism? I recently wrote about Aristotle's mistake, which was carried through the centuries. You replied that it was "obvious" why this was not set later. And I agree with you, this is precisely what dogmatism is-a brake on progress. Science does not develop evenly, it is characterized by bursts, jumps, flips, if you will. And as a rule, after such bursts, there is a slow use of the existing paradigm. This is exactly what I meant when I spoke about the lack of direct historical continuity between cultures. Because these jumps are not characteristic of any particular culture, but of humanity as a whole. Here's an example with Nazarov. Even Severtsov paid tribute to the book - this is the second experience in Russian literature to collect all the alternative theories of the development of organisms! Second, after Schmalhausen. What, is Darwin's theory so infallible that there are no buts, ifs, or maybe's? On the contrary, Darwin developed his theory based on the data obtained by him only for a single trip around the world! And then a whole galaxy of the smartest people of the 20th century developed STE in order to smooth out the corners, this polygonal structure called the theory of evolution. I don't want to say that the theory is bad, not at all. It was revolutionary for its time, it was precisely the adaptation that allowed us to look at things differently, not as they were taught in theological schools. And this work was then also compared to the devilry that you wrote about. You were amused by the phrase that Nazarov has embarked on a difficult path. Does it bother you that a doctor of science or a leading researcher puts his career, title, or position in question for the sake of publishing a popular book with dubious content? As a scientist, you are not interested in this fact, since it does not fit into the well-written structure of the world taught at Moscow State University and other reputable universities? What can I say, you don't even want to read it!!! Isn't that dogmatism?
And yet, going back to the beginning of the dialogue, I do not say in any way that your position on the naturalness of taxonomy is wrong in principle. Of course not! But I will return to my first thesis-taxonomy is not natural at the present time, and probably it will never be so, but the very idea of naturalness is akin to the idea of a bright future, to which we have all been moving for so long .

And in Europe 300 years ago, thank God, no one was burned. 300 years ago, Carl Linnaeus was born.

Ah, well, add another 200 years and I'll be right.

A hypothesis remains a hypothesis, whether it has been challenged or not. I still think that two hypotheses are described, if only because the recognition of the first one must necessarily lead to the disbandment of the taxon, and the second one is not necessary.

There are only two points of view: whether reptiles are polyphyletic or not polyphyletic. Their paraphilia (although this is a hypothesis) is absolutely obvious, since no one has yet been able to deduce birds and mammals from reptiles. I gave a quote about the polyphyletic nature of reptiles from a book by PIN's collaborator K. Y. Eskov.

So, according to you, we have two advantages. I will illustrate them by comparing them with the concept of a Natural System (not necessarily phylogenetic). Sorry for the monkey business in the first case.

You have replaced the word " phylogeny "with the words"natural system". That is, you believe that it exists in nature in addition to us, and in your manual it is said that the natural system should reflect natural laws that exist in addition to us. Please explain, if there is a "Natural System" in the first sense, how does it differ from phylogeny, and if it does not exist, what patterns should it reflect?

The natural System is constructed in such a way that taxa are located "at the points of maximum extrapolation", so its predictive ability is just a tautology and does not need to be justified at all.

In my opinion, it is obvious that the "extrapolation principle" itself does not make sense. Predictive behavior depends on which group we have placed the taxon in and the principles on which we have placed it there. For example, if you place a primarily wingless genus in the paraphyletic taxon Apterygota, you will not be able to determine with any certainty what kind of oral apparatus it has: mastoid or postmandibular. And if you place a taxon in a group based only on similar characteristics, then there is also no question of extrapolation: I recently gave an example with the Aptera taxon. But in phylogenetic classification, the idea of extrapolation makes sense. Yes, please explain what "maximum extrapolation points" are and how taxa can be placed in them.

This is not an argument. There are different approaches to linguistics

Yes, you never know what is considered normal in linguistics, geology,astronomy and carpentry. In the era of the phylogenetic approach, many classifications were created because of computer cladism: taxonomy became available to a wide range of untrained researchers, who in a few months began to fabricate work that would take years and decades to complete. The phylogenetic approach itself has nothing to do with it. It's like blaming a gun for some idiot killing a man with it. Well, to say that Linnaeus would have created a natural or" very decent " system, it is necessary to first determine what a "natural system"is.

Are there many studies that prove the link between hiatus and reproductive isolation? There may be hiatus, but there is no reproductive isolation (and vice versa).

The connection between reproductive isolation and hiatus is, of course, not absolute; it is deduced logically and shown on a fairly large material. In addition to this criterion, a geographical one is used. And how do molecular differences fundamentally differ from morphological hiatus? In general, I am talking here about the classification of ANIMALS, not fungi, plants, bacteria or viruses. For me, it is not at all obvious that for all these groups the concept of species and approaches to classification should be the same, and even close to those in linguistics and geology.

Ivakhnenko's concept was very beautiful, but it was not accepted by foreign paleontologists.

You never know what someone did not accept - this is not an argument. For example, many foreign taxonomists accept the Uniramia taxon; should we follow their example? Well, let them, anapsids, criticism of this idea Ivakhnenko does not refute the idea of polyphyletic reptiles, which we consider in the traditional sense, because it is clear that when this taxon is disbanded, monophyletic reptiles will still remain.

The Pancrustacea concept is probably the case here,

No, they did, but the histology of the suprapharyngeal ganglion and the "4 genes" did not outweigh the loss of the second antennae, the nandibular palpel, the two-branched limbs, the extensor muscle of the claw, the presence of ectodermal malpighian vessels and the parietal organ. It's the same with annelike dust.

About Aristotle. His system did not survive until the 19th century.

Division of animals into bloodless (invertebrates) and animals with blood (vertebrates) just the same and survived. The latter he divided into fish, birds, mammals (well, whales mistakenly separated into a separate group) and amphibians and reptiles. Its Entomon corresponds to Tracheata, Malacostraca to crustaceans. What I was wrong about was that I couldn't check the stories of travelers and other fishermen.

Have you seen a real phylogenetic tree? Then tell us

It doesn't matter how the types were created. There are no real, natural boundaries between them, only their position on the phylogenetic tree and apomorphic features. If you really want to, you can call the latter borders.

Darmidont

If you want to get an opinion on the weaknesses of Darwin's theory, then it is better to turn to the books of Tchaikovsky (and if you talk about this topic, then the evolutionary forum at the Paleontological Institute is suitable). In Russia, STE is experiencing another wave of criticism. It's another matter if you want to tease Tentatora…


Tentator

Oh, my God! Once again, Reptilia, according to some authors, is a MONOPHYLETIC group that unites ALL amniotes except synapsids (*birds are also amniotes)

Ndaaa... In the case you described, reptiles are again polyphyletic, since they include all amniotes except synapsids, i.e., mammals that are descended from synapsids.

Proven by whom? Please provide links.

Charles Darwin. Origin of species by natural selection. Ernst Mayr. Zoological species and evolution. There are plenty of references in the latest book.

To begin with, animals are already an artificial group... Further: a number of animals do not have cross-fertilization at all. Bdelloid rotifers do not have males.

I mean, is Metazoa an artificial group? There are always exceptions. Once again, wildlife is not a periodic table.

Well, with two-branched limbs, it's empty. Losing something isn't exactly an apomorphy. This leaves a very modest number of apomorphies. I'm not talking about annelid and arthropod synapomorphies - you'd better not get involved here at all, since you're obviously not competent to write about two-branched limbs.

Why can't the loss of any structure be a reliable apomorphy? Whether the limbs of arthropods were originally two-branched is an open question, and it is possible that they were. If you have a competent revelation on this subject, please share it!

These are all empty words, since apomorphism is a pure convention. Even the most inveterate cladists are forced to accept the existence of structural plans that are unified within metasome types and supertypes.

We are talking about supraspecific taxa, not races, nations, or populations. Yes, for example, mammals do not exist, but there is a phylogenetic branch (or branches) and a collection of species that we combine under the name overhanging. A building plan is just a combination of apomorphic and plesiomorphic features. Who has to admit it, if many of the guys with these strony plans of theirs are bursting at the seams? It's funny, you don't recognize the boundaries between species, but you persist in asserting the actual boundaries of other taxa. If these boundaries are real, then why not draw them on every node of the tree or on every apomorphy, as the cladists you hate demand?

There are only two points of view: whether reptiles are polyphyletic or not polyphyletic.

That's right. I'm glad you agreed with me.

That's right. I'm glad you agreed with me.

Yes, but if I understand you correctly, you were talking about the paraphyletic-polyphyletic taxon alternatives, not the polyphyletic-non-polyphyletic one. It's not the same thing.

Yes, I am familiar with this book, and it is not for nothing that in the preface to my gratitude I asked you to provide links to some more or less modern scientific publication.

I do not study vertebrates and am not familiar with the latest literature on this topic, but I have no reason to distrust an academic institute employee who receives first-hand information from his colleagues. Besides, since you know K. Y. You can ask him personally about the state of affairs in this area.

a) "Top": different picture. The EF is closer to history, while the EU is closer to geography. Of course, there are no sharp boundaries here, but the principles of organizing knowledge are different.

Now I don't understand you. What is the essence of this Natural System, which is almost identical to phylogeny, and how is it related to geography and what does phenetics have to do with the natural system?

b) "From below": different algorithms.

And I also don't understand why in taxonomy, if it's not about molecular data, computer methods are needed? It is quite possible to analyze all the essential signs, even a large number of them, in your mind and with your hands. In any case, computer methods are secondary to the essence of approaches.

Not quite so: by placing a certain taxon in Apterygota, we can predict, for example, the small size (first millimeters)of an individual.

Alas, even this is not the case: bristle-tails reach 2 cm in length.

Do you agree that the more we can predict, the more natural the taxon is? OK, so you think the whole idea of extrapolation needs some justification, right?

Yes, but on the contrary, the more natural a taxon is, the more we can predict. Pre-narrativeness is a consequence and it is not absolute even if the taxon is as natural as possible, so it cannot serve as a basis for verifying naturalness.

About Darwin's views on the boundaries of species and subspecies, you are confused. Here is a link to the chapter "Hybridization" in the Origin of Species: http://charles-darwin.narod.ru/chapter9.html and for comparison, a modern work on the issue under discussion: http://macroevolution.narod.ru/fridman.doc. Another of the latter is the work of V. A. Lukhtanov Lukhtanov V. A. et al., 2005. Nature. V. 436. P. 385-389( I do not have the article itself, but here is an excerpt from its review: Despite its simplicity, wide popularity and numerous attempts to verify, the hypothesis of increased prezygotic isolation did not have a reliable empirical justification until recently, and such a speciation mechanism was generally considered unlikely or rare. However, this hypothesis was tested and received convincing confirmation in the work of V. A. Lukhtanov from St. Petersburg University, N. P. Kandula from Harvard and their colleagues, using the example of several dozen closely related species and
subspecies of pigeon butterflies (family Lycaenidae) from the genus Agrodiaetus...)

Because loss is a simple evolutionary modus. which can occur repeatedly. In arthropods, gills, tracheae, AI, abdominal limbs, etc. are lost independently in different groups.

However, the tracheae and especially the gills, as well as the Malpighian vessels (though from different germ sheets) in arthropods also arise independently several times. What, then, is the fundamental difference between loss and arising?
The frequency of loss and occurrence of something is checked by other signs.

A building plan is an architectonic concept, and feature states are part of tectology; you can't lump everything together.

For God's sake. But tell me, what does the structure plan provide for taxonomy? How can it serve as a proof of the naturalness of the taxon?

Hennig believed that the "ancestor-descendant" relationship cannot be accurately reconstructed, and if you hold a similar opinion, you only sign that it is impossible to reconstruct the true phylogeny, i.e., it is impossible to build a natural (in your understanding) system.

The meaning of these words is that any taxon comes from a certain species and even more precisely from certain populations. Of course, it is impossible to trace all genealogical connections at this level, but this does not contradict the idea of a natural system.

This is a difficult question. On the one hand, you're right. For example, Darwin's theory, although quite natural, is not able to predict the outcome of macroevolution.

Evolutionary theory is not able to predict the outcome of macroevolution because it cannot take into account all the factors that influence the process of evolution: there are a huge number of them, they are different for different taxa, and most of them are not known. And with regard to the predictivity of natural taxa, this is not idle speculation; I encounter this very often: without having certain representatives of the group I have identified and receiving them later, I find in them signs that I assumed in advance, and, for example, in the genitals, which no one before me in these groups at all I watched it. I don't want to brag, but I rarely make mistakes. Perhaps this is a specific feature of the group.

Finally, to end the subject of reptiles, I present a phylogeny with the boundaries of reptiles in your understanding. Synapsids are an ancestral group for mammals, diapsids are an ancestral group for birds. Perhaps our differences are limited only to the understanding of volumes, i.e. the inclusion or non-inclusion of Mammalia and Aves in Synapsida and Diapsida, respectively. Then this situation is akin to Putinitsa in the Russian "Animal Life", when the name Apterygota was transferred to Triplura when this taxon was disbanded, or when the name Insecta is used for the taxon Ectognatha. Either you need to change the names of taxa when the volume changes, or you need to specify the volume specifically.

Pictures:

rept.jpg — (77.22к)

 
2) History and geography are metaphors. Need to explain further?

Yes, please explain. Metaphors suggest a free and poetic understanding, and I would like to understand you correctly.

Only in the sense of "phenetic systematics", that is, a classification procedure that does not weigh similarities based on their history.

What this leads to is scary to think about.

It is very sad that I often come across this point of view. I am only a little pleased that it is endemic to Russia (If necessary, I can argue and reveal my idea in more detail).

I will be very grateful to you.

OK, got it. So you put the prediction at the end, and I put it at the beginning.

Any law in science has predictive power, it is the consequence of the law, and the effect is never more primary than the cause. Only one sequence is possible: facts--law (system)--predictivity.

Please answer another question that I asked in the previous post.: You ask, what is a Natural System - some objective reality, or our ideas about it?

Yes, I'm asking. In my dissertation, without much thought, I named the chapter "History of studying the system". My supervisor corrected this title to "classification history", saying that we are not studying the system, but building it. I agree with this, because I believe that the classification should not be absolutely identical to phylogeny.

I quote from Darwin:

It is impossible not to notice how firmly Darwin actually distinguishes between the concepts of "species" and" variety "both in" Origin " and in other works. Krasilov probably correctly explained this difference in Darwin's stated and actual positions: "This apparent contradiction reflects, on the one hand, the internal inconsistency of the continuously intermittent process of speciation, and on the other, the discrepancy between the views of Darwin the philosopher and Darwin the naturalist. As a man of his time, he was influenced by the idea of continuity, gradual development (in particular, England from Queen Elizabeth to Queen Victoria), which was based on the mental balance of the Victorians. These views were supported by Ch. Lyell in his polemic with J. Cuvier, which included Darwin, who accepted the thesis of his senior colleague about the imperfection-pseudo-discontinuity — of the geological record. He concludes "The Origin of Species" with the Victorian's heart-warming assurance that life is gradual and that there is little chance of past or future disasters. At the same time, as an experienced taxonomist, Darwin could not help but realize that the idea of continuous change devalues species."

Independent occurrence of similar structures suggests that we can find differences in their structure

First, independent losses tend to have rudiments that differ in structure. And the independence of total losses is checked in the analysis of inherited traits, although, of course, such losses cannot be considered as the only apomorphies of a particular taxon. In the example you gave, the lack of trunk division into chest and abdomen is independently acquired by remipeds and millipedes, because firstly, remipeds never have diplosegmentation (since the number of segments they have can be both even and odd), whereas all millipedes are characterized by diplosegmentation. Secondly, it seems that cephalocarids are more primitive (their maxillae II do not yet differ from the legs of the following segments) than remipeds, and their body consists of 3 tagmas.

In taxonomy, it plays a role at the macro level

In taxonomy, it will not play a role at any level. A "group of images with a single structure plan" can be either natural or artificial. This concept is more appropriate even for a grad than a taxon, because it reflects a certain level of organization.

This is not the reason: the essence of STE is stochasticity and nonlinearity.

Stochasticity is a concept that makes sense if there is incomplete knowledge about the causes, even in the case of nonlinear systems. Opponents of Darwinism imagine the world in the form of a simple magic kingdom, in which instead of a large number of complex unknown laws and causes, a couple of simple magic acts.

I reread Darwin

"To sum up, I believe that species are made into something with well-defined boundaries and do not represent an unsolvable chaos of insensibly changing and intertwining links" ("The Origin of Species". Grava 4).

In cases where two related groups independently enter the path

They may or may not be. Independently formed structures may also have few structural details and be completely indistinguishable in different groups. If you analyze only one single trait, then of course, the devil knows: it arose or was lost, independently or was inherited from a common ancestor, but no one analyzes a single trait; there are many signs and usually there are some, at least initial ideas about phylogeny, on the basis of which you judge the evolution of a given one. of the attribute.

Only diplopods have diplosegments.

Yes, of course, diplosegmentation here does not prove anything solid, but such a difference in the body structure of remipeds and millipedes suggests that homonomy in these groups may have some different nature. Analysis of other traits and the phylogenetic hypothesis based on it suggest that remipeds are not the most primitive group of crustaceans: maxillae are generally quite similar to legs, but in remipeds they differ from the trunk legs by single-branching (in cephalocarids they are two-branched), and the trunk legs are swimming, unlike the walking legs of trilobites and many crustaceans. Even in millipedes, diplopods with pauropods have one suspicious property: behind the collum they have 3 haplosegments, i.e. like insects...

"mad" Beklemishev

Not convinced. Beklemishev wrote a wonderful book on comparative morphology; in this discipline, the concept of structural plan is very important, but what it does for taxonomy you have not explained. Let bilaterality be the essence of a structural plan, or something else, but for taxonomy, only the state of this trait in a particular group makes sense.

Did you summon Dormidont

Well, first of all, I didn't encourage Monsieur Dormidont to educate himself, but only responded to his remark about textbook truths-what you need to do to make "truths" really true. Secondly, science has not abandoned the "principle of causality"; it is just that in synergetics, in which you are so well versed, this causality has acquired a much more complex and universal understanding. You will laugh, but causality in synergetics is perfectly explained in Aristotelian terms of causality (see, for example, here: http://www.philsci.univ.kiev.ua/biblio/Dobr-practphil.html). However, I must repeat to you what Monsieur Dormidontou said: I do not have enough leisure to discuss the problems of philosophy or synergetics and postmodernism here.

Yes, please explain. Metaphors suggest a free and poetic understanding, and I would like to understand you correctly.

OK. General phylogeny is a description of events, roughly speaking, who descended from whom. A natural system is a description of the structure, again roughly speaking, who is closer to whom. That's the story with geography.

OK. General phylogeny is a description of events, roughly speaking, who descended from whom. A natural system is a description of the structure, again roughly speaking, who is closer to whom. That's the story with geography.

Description of the structure of what? "Who is closer to whom" by what criteria? Phylogeny is also "who is closer to whom"

Plantago
I'm not sure it disciplines the mind.

All of this is absolutely true.

We read in chapter XV, where everything is summed up

And yet it does not follow that

Darwin considered the species a convention

I repeat: you only think this way because you have experience working with a group with a complex morphology.

Yes, my views are not quite adequate for many groups, as well as yours - the other part of animal groups, which, by the way, are the majority. This is what I said from the very beginning: there can be no uniform principles of sysstematics for all living things.

You don't call for analyzing individual attributes, but you only analyze one of them. If we look at the other limbs

I'm taking information from a university course on arthropod evolution. You asked me to explain whether the primary metamericity of the torso in remipeds and millipedes is primary-I explained it on the basis of one of the alternative hypotheses. The hypothesis you describe is no more than a true one. Why did the juvenilization of the remipeds, which supposedly led to the consolidation of metamericity in the adult phase, not lead to the consolidation of the two-branched maxillae present in nauplius? The specialization of cephalocarid sperms does not confirm anything particularly, unless it is synapomorphy with other crustaceans. I don't want to touch on these questions, but still, aren't branchiopods specialized with their swimming undifferentiated single-branched legs, preserved only on the chest and greatly simplified maxillae? Molecular data is great, but in some studies, beetles are bred from bedbugs based on them...

Let me explain with a concrete example.

Juglans, this argument is not very reasonable, because we disagree on the fundamental vision of the system, hence the differences in details. However, there is a contradiction in your own reasoning: the Articulata supertype has its own structural plan, which does not save this taxon from being disbanded based on molecular data, which are separate characters.

In fact, any mediocre researcher can isolate signs and conditions, drive them into a matrix and conduct an analysis.

Oh, yes, that's true. A computer can't replace your head. But I wrote about something else, about the benefits of computer methods in general!

Description of the structure of what? "Who is closer to whom" by what criteria? Phylogeny is also "who is closer to whom"

Here! It's getting warmer! Similarity-it can be different. Historical similarity is modeled by a graph arc (oriented connection), and geographical similarity is modeled by a graph edge (undirected connection).

plantago

Naturally, molecular methods cannot but be based on computer processing, but I wrote about morphology... As for birds, before molecular trees, their phylogeny was far from what cladists now imagine it to be. And in the case of flowering plants, everything was far from so clear (at least I do not believe that morphological cladistic analysis brought plane trees and lotus trees closer together). Already after molecular trees morphological cladograms began to be "tightened" by manipulating characters and taxa. Even a paper was published in which ecdysozoa were isolated in a morphological computer cladogram! (and it was made ugly). Cladists like to "cross" molecular and morphological trees into one, showing high support for many clades, but this all looks very, very strained exactly where before the pure morphological cladograms were very different. These are now acelomorphs - the most archaic bilaterians, but before molecular methods, the Ehlers cladogram was used as a basis, in which acelomorphs were separated later than catenulids. And, after all, even Mamkaev and Ivanov proved that the absence of nephridiums in acelomorphs is a primary condition! Only a few foreign zoologists believed in this "Russian reserve of phagocytellar theory".

.. I don't believe that morphological cladistic analysis brought sycamore trees and lotus trees closer together.

You took an extreme example. By the way, fossils of sycamores shed some light on this terrible pair: they have a plentiful perianth, apocarpic gynoecium, and other signs of lotus (Manchester, 1986; Magallon-Puebla et al., 1997). If these data were taken into account by Nandi et al. (1998) or Hufford (1992), it is possible that sycamore trees would be grouped with lotus trees. But the main advantage of the cited works is that the trees there are closer to molecular ones than the constructions of evolutionary taxonomists (except perhaps R. Dahlgren).
In fact, I don't want to argue so much as discuss this problem. It is true that morphological and molecular cladograms do not coincide - why? Maybe it's not just the lack of qualifications of morphologists? Are C. Nielsen or P. Endress so unqualified? Or P. Ax? I'm not going to do an analysis of the most" molecular-adequate " morphological features in flowering plants, even if I received all the data from Ovi Nandi... No one is interested in this here?

Not just on the chest

The conversation drifted away into private matters. I think that in the case of millipedes and remipeds, it is equally difficult to prove both the primacy of homonomy and its secondary nature, i.e., both the loss of a trait and its occurrence. But it seems that we have come to a consensus here anyway: to a certain extent, approaches to building a system are determined by the specifics of the group. And thank you for telling me about crustaceans. I will definitely start self-education in connection with this group.

Here! It's getting warmer! Similarity-it can be different. Historical similarity is modeled by a graph arc (oriented connection), and geographical similarity is modeled by a graph edge (undirected connection).

Mathematics is a tool that serves a specific purpose. No tool should be made into a fetish: if it is adequate to its purpose, it is good; if it is not adequate , it is bad. The goal of taxonomy is to build a system, and understanding this goal should be primary, and not a tool from whose functions the goal that it should serve is derived. It seems to me that your "Natural System" is such an artificial, fictitious goal: there is no law that would connect" geographically " the characteristics of living organisms by themselves, without connection with the historical development of the carriers of these characteristics.

plantago
do not find time in vain: what "sinks" in America will cause a resonance in Russia. Your system in JOBe and Antonov's criticism in Bot. zhurnal are even analyzed at special seminars in provincial universities - Can you imagine that this will happen to you in the United States?


About discrepancies. Note that they are smaller the younger the group, the more complex it is, the more morphologically studied it is, and the molecular data (for several genes and long sequences) relate to a large number of different species. For example, you can already build a tree based on only one carpology in flowering plants, but for the same ticks, try using the structure of the reproductive system and sperm: you will not succeed, because there is simply no data. For many groups, it is sufficient to study the external structure. In many cases, there are simply few signs (for example, in protists). In many cases, there are enough features, but due to the abundance of fossil material, the emphasis is placed on skeletal structures (mollusks, reptiles, bivalves, bryozoans). Rasnitsyn published a good article in his time: he showed discrepancies between the molecular tree, the morphological tree based on the morphological data of review forms, and the morphological tree based on review and fossil forms of hymenoptera. Indeed, vertebral paleontologists are now simply forced to "not see" parallelisms, since this does not correspond to the economical paradigm. The monophyly of tetrapods is still a very dubious thing, which was written about both in the West and in our country. Meijen has the "empathy principle": let's mentally "sympathize" with Kurochkin's bird evolutionary scheme and you can see arguments in it that cannot be tested in molecular terms. But, after all, non-cladists are no longer sympathized with....

Another problem is the topology of cladograms in the basal part. It is still unresolved and there is no paradigm that can solve it. Neither for flowering plants nor for arthropods, and molecular data here do not give much. Then suddenly the colemboles fall into crustaceans, then suddenly the ctenophores are older than the sponges. Such "fluctuations" are published in a "wave", although they are only those that must first be thoroughly checked (changing external groups, tree construction algorithms, etc.), and then formalized in an article. Such "noise" is so great that different molecular trees threaten to overlap all existing morphological tree discrepancies. Then the problem "morphology-molecular methods" will move to the right.

And how do you define the "adequacy" or "non-adequacy" of mathematical methods in phylogenetics?

Tentator

there is no law that would link" geographically " the characteristics of living organisms in themselves, without connection with the historical development of the carriers of these characteristics.

This is a philosophical question, in the full sense of the word. I believe that such a law exists.

plantago
do not find time in vain: what "sinks" in America will cause a resonance in Russia. Your system in JOBe and Antonov's criticism in Bot. zhurnal are even analyzed at special seminars in provincial universities - Can you imagine that this will happen to you in the United States?

Thank you, didn't know, flattered
I'm mostly in America for family reasons.
Your opinion is very valuable to me -- I will try to change my priorities a little.

This is a philosophical question, in the full sense of the word. I believe that such a law exists.

Well, philosophy is also not an area of absolute mental arbitrariness.

Was that a question for me?

No, I think it's for me. The best way to determine the adequacy of a tool is based on the results of its use. There is a lot of absurd waste paper written using computer methods in cladism. It is these works that discredit Cladism in the eyes of its honest opponents. I won't deny the potential for the mathematical future of phylogenetics and taxonomy, but I don't see the reasons for it yet.
They made me laugh about the incompetence of morphologists. This is compared to the competence of molecular scientists, who do not know groups, but know mathematics?
About the discrepancy between "molecular" and "morphological" cladograms: if you take two sets of 2-3 signs and build cladograms from them, then such cladograms will almost never coincide. I'm exaggerating, of course, but how do some of the genetic material used by molecular scientists compare with a set of traits from various organ systems used by morphologists?

No, another: "Chronicle and cladogram" (2006) / / Evolution of the biosphere and biodiversity. KMK

Thanks! I found it on his website.

plantago
that's not what I'm talking about. By what criteria do we determine that, for example, bootstrap, as a mathematical method, is adequate for evaluating monophilia?

Bootstrap does not evaluate monophyly, it evaluates the stability of nodes on a cladogram.

But through this stability, the researcher estimates the probability of monophilia... After all, we are talking about transferring a purely mathematical algorithm to the biological sphere. The question is, why is bootstrap support considered "good" in 85%, and not very good in 55%? You can select 15 features and get a very allowed tree, or you can add 15 more features and the tree becomes less allowed. Where is the guarantee that the researcher does not" fit "the matrix to bootstrap, believing that he throws out"bad signs"?

Yes, this is a very important question. All such methods imply much greater freedom, including, unfortunately, in fitting the results. There are few publications on this subject (three in the appendix).
But the same question arises in "simple" statistics - why should p be < 0.05?! The answer is one - based on existing experience. Similarly, a researcher can narrow down the sample by achieving the desired 0.05...

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Shoffer - we are talking about types, classes, and squads.

First of all, it is not necessary at all.
And secondly, I don't see a fundamental difference.
Well, unless the ICZN can't reach you. But colleagues are also not asleep.

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